将txt文件加载到GSEA时出现Java错误
将txt文件加载到GSEA时出现Java错误
提问于 2016-12-07 04:32:48
我正在尝试上传一个包含基因表达数据的text file，以便使用GSEA进行分析，但我得到了以下Java错误：
<Error Details>
---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.lang.NumberFormatException: ...
---- Stack Trace ----
# of exceptions: 1
------For input string: "NA"------
java.lang.NumberFormatException: For input string: "NA"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseFloat(FloatingDecimal.java:122)
at java.lang.Float.parseFloat(Float.java:451)
at edu.mit.broad.genome.parsers.TxtDatasetParser._parseNoDesc(TxtDatasetParser.java:178)
at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:140)
at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:96)
at edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:455)
at edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:410)
at edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:406)
at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:1897)
at edu.mit.broad.genome.parsers.ParserFactory$1.run(ParserFactory.java:2766)
at xapps.api.AppDataLoaderWidget$2.actionPerformed(AppDataLoaderWidget.java:251)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.Component.processMouseEvent(Component.java:6533)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6298)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)我的文本文件是从R保存的，包含以下内容:带有基因ID的'NAME‘列，带有'NA’的'DESCRIPTION‘列，以及带有相关基因计数信息的样本1-30。
> head(IL2.ZAvsIL2_GSEA)
NAME DESCRIPTION SM01 SM02 SM03 SM04 SM05 SM06 SM07 SM08 SM09 SM10 SM11 SM12
1 MRPS6 NA 457 905 660 685 656 650 1361 1019 1421 1006 510 1182
2 APP NA 199 191 210 196 200 179 235 225 252 228 159 95
3 POLR3GL NA 800 658 763 655 602 814 866 709 1141 802 743 545
4 OMA1 NA 233 758 958 709 747 206 851 876 1272 832 239 821
5 TSC22D1 NA 426 456 577 441 433 390 579 646 709 504 580 574
6 ARRDC3 NA 6073 1496 2128 1706 1435 6033 2761 3238 4390 3306 6216 2359
SM13 SM14 SM15 SM16 SM17 SM18 SM19 SM20 SM21 SM22 SM23 SM24 SM25 SM26 SM27 SM28
1 1305 909 944 423 812 595 673 527 441 495 562 633 738 895 1571 1255
2 387 253 200 121 85 130 116 133 288 194 267 241 395 178 119 239
3 1179 707 765 1032 675 671 908 754 1345 531 877 896 1073 1444 765 1085
4 1183 879 904 219 731 911 1043 898 357 699 1069 1021 1374 272 960 1136
5 1151 799 884 420 462 594 543 421 715 486 586 506 900 822 624 768
6 4479 3376 3449 6656 954 1181 1682 1221 8437 912 1808 1819 2172 7182 1560 2173
SM29 SM30
1 1022 1307
2 187 242
3 907 905
4 975 1217
5 649 761
6 1918 2063
> write.table(IL2.ZAvsIL2_GSEA, file="IL2.ZAvsIL2_GSEA.txt",row.names = FALSE,sep = "\t") 看起来Java抛出了一个格式错误，因为在'DESCRIPTION‘列中找到了’NA‘，但我不知道如何纠正这个问题。
回答 2
Stack Overflow用户
发布于 2017-12-02 13:49:33
解析器区分大小写。把你的'NA‘改成'na’来修复。
write.table(IL2.ZAvsIL2_GSEA, file="IL2.ZAvsIL2_GSEA.txt",row.names = FALSE,sep = "\t", na.strings = "na")Stack Overflow用户
发布于 2019-10-19 04:42:27
我也有同样的问题，即使使用A.liberzon提到的"na“技巧，我仍然得到一个错误。我在Description列中输入了一个数值(即df$Description <- 1)，它加载得很好。
页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持
原文链接：
https://stackoverflow.com/questions/41004336
复制相关文章
相似问题
腾讯云开发者
